1 answer

For BAM files the options available for visualization can be found in the control and options menus for the plots. Current those options only include Emphasis and Stacking options for coloring and drawing the reads in the pileup plot as well as some filter and quality shading is also available. You can find these options by clicking the gear icon in the upper left corner of the pileup plot or by going to View > Dock Window > Controls to make the options tabs visible for the plot.

We have been considering allowing for the option to color and filter by other BAM properties such as the read group field but that functionality is not currently available.

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